No, there is not an easy way to achieve this. You usually don't access the inbox of users as this data is sensitive.
The most simple way I can think of is to delete the whole mailbox and reimport it.
(But somehow I have the feeling you can't do that because the users are already using the new mail-environment)
Here is a technet aricle which describes how to remove duplicates in Outlook: How to remove duplicate imported items in Outlook
Anywho, you have to open up each inbox to find the duplicates. You could script this using powershell: Get-MailboxFolder
$inbox = Get-MailboxFolder -Identity $_:\Inbox
....do something with inbox here...
But for help with a script, I would ask on http://www.stackoverflow.com